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Martínez-Magaña JJ, Hurtado-Soriano J, Rivero-Segura NA, Montalvo-Ortiz JL, Garcia-delaTorre P, Becerril-Rojas K, Gomez-Verjan JC. Towards a Novel Frontier in the Use of Epigenetic Clocks in Epidemiology. Arch Med Res 2024; 55:103033. [PMID: 38955096 DOI: 10.1016/j.arcmed.2024.103033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/10/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
Health problems associated with aging are a major public health concern for the future. Aging is a complex process with wide intervariability among individuals. Therefore, there is a need for innovative public health strategies that target factors associated with aging and the development of tools to assess the effectiveness of these strategies accurately. Novel approaches to measure biological age, such as epigenetic clocks, have become relevant. These clocks use non-sequential variable information from the genome and employ mathematical algorithms to estimate biological age based on DNA methylation levels. Therefore, in the present study, we comprehensively review the current status of the epigenetic clocks and their associations across the human phenome. We emphasize the potential utility of these tools in an epidemiological context, particularly in evaluating the impact of public health interventions focused on promoting healthy aging. Our review describes associations between epigenetic clocks and multiple traits across the life and health span. Additionally, we highlighted the evolution of studies beyond mere associations to establish causal mechanisms between epigenetic age and disease. We explored the application of epigenetic clocks to measure the efficacy of interventions focusing on rejuvenation.
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Affiliation(s)
- José Jaime Martínez-Magaña
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; U.S. Department of Veterans Affairs National Center for Post-Traumatic Stress Disorder, Clinical Neuroscience Division, West Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | | | | | - Janitza L Montalvo-Ortiz
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; U.S. Department of Veterans Affairs National Center for Post-Traumatic Stress Disorder, Clinical Neuroscience Division, West Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | - Paola Garcia-delaTorre
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Área de Envejecimiento, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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2
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Singh M, Dolan CV, Lapato DM, Hottenga JJ, Pool R, Verhulst B, Boomsma DI, Breeze CE, de Geus EJC, Hemani G, Min JL, Peterson RE, Maes HHM, van Dongen J, Neale MC. Twin-based Mendelian Randomization Analyses Highlight Smoking's Effects on Blood DNA Methylation, with Putative Reverse Causation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.19.24309184. [PMID: 38946972 PMCID: PMC11213072 DOI: 10.1101/2024.06.19.24309184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Epigenome-wide association studies (EWAS) aim to identify differentially methylated loci associated with complex traits and disorders. EWAS of cigarette smoking shows some of the most widespread DNA methylation (DNAm) associations in blood. However, traditional EWAS cannot differentiate between causation and confounding, leading to ambiguity in etiological interpretations. Here, we apply an integrated approach combining Mendelian Randomization and twin-based Direction-of-Causation analyses (MR-DoC) to examine causality underlying smoking-associated blood DNAm changes in the Netherlands Twin Register (N=2577). Evidence across models suggests that current smoking's causal effects on DNAm likely drive many of the previous EWAS findings, implicating functional pathways relevant to several adverse health outcomes of smoking, including hemopoiesis, cell- and neuro-development, and immune regulation. Additionally, we find evidence of potential reverse causal influences at some DNAm sites, with 17 of these sites enriched for gene regulatory functional elements in the brain. The top three sites with evidence of DNAm's effects on smoking annotate to genes involved in G protein-coupled receptor signaling (GNG7, RGS3) and innate immune response (SLC15A4), elucidating potential biological risk factors for smoking. This study highlights the utility of integrating genotypic and DNAm measures in twin cohorts to clarify the causal relationships between health behaviors and blood DNAm.
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Affiliation(s)
- Madhurbain Singh
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
| | - Conor V. Dolan
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Dana M. Lapato
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Brad Verhulst
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, College Station, TX, USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Current address: Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
| | - Charles E. Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
- UCL Cancer Institute, University College London, London, UK
| | - Eco J. C. de Geus
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Josine L. Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Roseann E. Peterson
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Hermine H. M. Maes
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- These authors jointly supervised this work
| | - Michael C. Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- These authors jointly supervised this work
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3
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Choudhary P, Monasso GS, Karhunen V, Ronkainen J, Mancano G, Howe CG, Niu Z, Zeng X, Guan W, Dou J, Feinberg JI, Mordaunt C, Pesce G, Baïz N, Alfano R, Martens DS, Wang C, Isaevska E, Keikkala E, Mustaniemi S, Thio CHL, Fraszczyk E, Tobi EW, Starling AP, Cosin-Tomas M, Urquiza J, Röder S, Hoang TT, Page C, Jima DD, House JS, Maguire RL, Ott R, Pawlow X, Sirignano L, Zillich L, Malmberg A, Rauschert S, Melton P, Gong T, Karlsson R, Fore R, Perng W, Laubach ZM, Czamara D, Sharp G, Breton CV, Schisterman E, Yeung E, Mumford SL, Fallin MD, LaSalle JM, Schmidt RJ, Bakulski KM, Annesi-Maesano I, Heude B, Nawrot TS, Plusquin M, Ghantous A, Herceg Z, Nisticò L, Vafeiadi M, Kogevinas M, Vääräsmäki M, Kajantie E, Snieder H, Corpeleijn E, Steegers-Theunissen RPM, Yang IV, Dabelea D, Fossati S, Zenclussen AC, Herberth G, Magnus M, Håberg SE, London SJ, Munthe-Kaas MC, Murphy SK, Hoyo C, Ziegler AG, Hummel S, Witt SH, Streit F, Frank J, Räikkönen K, Lahti J, Huang RC, Almqvist C, Hivert MF, Jaddoe VWV, Järvelin MR, Kantomaa M, Felix JF, Sebert S. Maternal educational attainment in pregnancy and epigenome-wide DNA methylation changes in the offspring from birth until adolescence. Mol Psychiatry 2024; 29:348-358. [PMID: 38052982 PMCID: PMC11116099 DOI: 10.1038/s41380-023-02331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
Maternal educational attainment (MEA) shapes offspring health through multiple potential pathways. Differential DNA methylation may provide a mechanistic understanding of these long-term associations. We aimed to quantify the associations of MEA with offspring DNA methylation levels at birth, in childhood and in adolescence. Using 37 studies from high-income countries, we performed meta-analysis of epigenome-wide association studies (EWAS) to quantify the associations of completed years of MEA at the time of pregnancy with offspring DNA methylation levels at birth (n = 9 881), in childhood (n = 2 017), and adolescence (n = 2 740), adjusting for relevant covariates. MEA was found to be associated with DNA methylation at 473 cytosine-phosphate-guanine sites at birth, one in childhood, and four in adolescence. We observed enrichment for findings from previous EWAS on maternal folate, vitamin-B12 concentrations, maternal smoking, and pre-pregnancy BMI. The associations were directionally consistent with MEA being inversely associated with behaviours including smoking and BMI. Our findings form a bridge between socio-economic factors and biology and highlight potential pathways underlying effects of maternal education. The results broaden our understanding of bio-social associations linked to differential DNA methylation in multiple early stages of life. The data generated also offers an important resource to help a more precise understanding of the social determinants of health.
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Affiliation(s)
- Priyanka Choudhary
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland.
| | - Giulietta S Monasso
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ville Karhunen
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Research Unit of Mathematical Sciences, Faculty of Science, University of Oulu, Oulu, Finland
| | - Justiina Ronkainen
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
| | - Giulia Mancano
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
| | - Caitlin G Howe
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Zhongzheng Niu
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - John Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Charles Mordaunt
- Department of Medical Micriobiology and Immunology, University of California Davis, Davis, CA, USA
| | - Giancarlo Pesce
- Epidemiology of Allergic and Respiratory Diseases (EPAR) team, Faculté de Médecine Saint-Antoine, Institute Pierre Louis d'Epidemiologie et Sante Publique (IPLESP), Sorbonne Université and INSERM, Paris, France
- Paris-Saclay University, Paris-South University, UVSQ, Center for Research in Epidemiology and Population Health (CESP), INSERM, Villejuif, France
| | - Nour Baïz
- Institute Desbrest of Epidemiology and Public Health, University of Montpellier and INSERM, Montpellier, France
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO-Piemonte, Torino, Italy
| | - Elina Keikkala
- Department of Obstetrics and Gynaecology, Research Unit of Clinical Medicine, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
| | - Sanna Mustaniemi
- Department of Obstetrics and Gynaecology, Research Unit of Clinical Medicine, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
| | - Chris H L Thio
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eliza Fraszczyk
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Elmar W Tobi
- Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, 3000 CA, Rotterdam, the Netherlands
| | - Anne P Starling
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marta Cosin-Tomas
- ISGlobal (Barcelona Institute for Global Health), Barcelona Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Jose Urquiza
- ISGlobal (Barcelona Institute for Global Health), Barcelona Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Stefan Röder
- Department for Environmental Immunology, Helmholtz Centre for Environmental Research, UFZ, Leipzig, Germany
| | - Thanh T Hoang
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Christian Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology, Section for Research Support, Oslo University Hospital, Oslo, Norway
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27606, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27606, USA
| | - John S House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27606, USA
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, 27709, USA
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Raffael Ott
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
| | - Xenia Pawlow
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
| | - Lea Sirignano
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anni Malmberg
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Phillip Melton
- Menzies Institute of Medical Research, University of Tasmania, Hobart, TAS, Australia
- University of Western Australia, School of Population and Global Health, Perth, WA, Australia
| | - Tong Gong
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ruby Fore
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Wei Perng
- Department of Epidemiology and the Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Zachary M Laubach
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Darina Czamara
- Department Genes and Environment, Max Planck Institute for Psychiatry, Kraepelinstrasse 2+10, 80804, Munich, Germany
| | - Gemma Sharp
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
- School of Psychology, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Carrie V Breton
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Enrique Schisterman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edwina Yeung
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20817, USA
| | - Sunni L Mumford
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20817, USA
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Janine M LaSalle
- Department of Medical Micriobiology and Immunology, University of California Davis, Davis, CA, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences, School of Medicine, University of California Davis (UC Davis), Davis, CA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Isabella Annesi-Maesano
- Institute Desbrest of Epidemiology and Public Health, University of Montpellier and INSERM, Montpellier, France
| | - Barbara Heude
- Université de Paris Cité, Inserm, INRAE, Centre of Research in Epidemiology and StatisticS (CRESS), F-75004, Paris, France
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Lorenza Nisticò
- Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Marina Vafeiadi
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Manolis Kogevinas
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigación Biomédicaen Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Marja Vääräsmäki
- Department of Obstetrics and Gynaecology, Research Unit of Clinical Medicine, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
| | - Eero Kajantie
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
- Clinical Medicine Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eva Corpeleijn
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Regine P M Steegers-Theunissen
- Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, 3000 CA, Rotterdam, the Netherlands
| | - Ivana V Yang
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Serena Fossati
- ISGlobal (Barcelona Institute for Global Health), Barcelona Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Ana C Zenclussen
- Department for Environmental Immunology, Helmholtz Centre for Environmental Research, UFZ, Leipzig, Germany
| | - Gunda Herberth
- Department for Environmental Immunology, Helmholtz Centre for Environmental Research, UFZ, Leipzig, Germany
| | - Maria Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie J London
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Monica Cheng Munthe-Kaas
- Department of Pediatrics, Oncology and Hematology, Oslo University Hospital, Oslo, Norway
- Norwegian Institute of Public Health, Oslo, Norway
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
- Technical University Munich, School of Medicine, Forschergruppe Diabetes at Klinikum rechts der Isar, Munich, Germany
| | - Sandra Hummel
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
- Technical University Munich, School of Medicine, Forschergruppe Diabetes at Klinikum rechts der Isar, Munich, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Innovative Psychiatric and Psychotherapeutic Research, Biobank, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Rae-Chi Huang
- Telethon Kids Institute, Perth, WA, Australia
- Edith Cowan University, School of Medicine and Health Sciences, Joondalup, WA, Australia
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marjo-Riitta Järvelin
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Marko Kantomaa
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Sylvain Sebert
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
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4
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Fang F, Quach B, Lawrence KG, van Dongen J, Marks JA, Lundgren S, Lin M, Odintsova VV, Costeira R, Xu Z, Zhou L, Mandal M, Xia Y, Vink JM, Bierut LJ, Ollikainen M, Taylor JA, Bell JT, Kaprio J, Boomsma DI, Xu K, Sandler DP, Hancock DB, Johnson EO. Trans-ancestry epigenome-wide association meta-analysis of DNA methylation with lifetime cannabis use. Mol Psychiatry 2024; 29:124-133. [PMID: 37935791 PMCID: PMC11078760 DOI: 10.1038/s41380-023-02310-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
Cannabis is widely used worldwide, yet its links to health outcomes are not fully understood. DNA methylation can serve as a mediator to link environmental exposures to health outcomes. We conducted an epigenome-wide association study (EWAS) of peripheral blood-based DNA methylation and lifetime cannabis use (ever vs. never) in a meta-analysis including 9436 participants (7795 European and 1641 African ancestry) from seven cohorts. Accounting for effects of cigarette smoking, our trans-ancestry EWAS meta-analysis revealed four CpG sites significantly associated with lifetime cannabis use at a false discovery rate of 0.05 ( p < 5.85 × 10 - 7 ) : cg22572071 near gene ADGRF1, cg15280358 in ADAM12, cg00813162 in ACTN1, and cg01101459 near LINC01132. Additionally, our EWAS analysis in participants who never smoked cigarettes identified another epigenome-wide significant CpG site, cg14237301 annotated to APOBR. We used a leave-one-out approach to evaluate methylation scores constructed as a weighted sum of the significant CpGs. The best model can explain 3.79% of the variance in lifetime cannabis use. These findings unravel the DNA methylation changes associated with lifetime cannabis use that are independent of cigarette smoking and may serve as a starting point for further research on the mechanisms through which cannabis exposure impacts health outcomes.
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Affiliation(s)
- Fang Fang
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA.
| | - Bryan Quach
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Kaitlyn G Lawrence
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jesse A Marks
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Sara Lundgren
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Mingkuan Lin
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
| | - Veronika V Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ricardo Costeira
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Linran Zhou
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Meisha Mandal
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Yujing Xia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jacqueline M Vink
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Laura J Bierut
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO, USA
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Dana B Hancock
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
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5
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Gilmore N, Loh KP, Liposits G, Arora SP, Vertino P, Janelsins M. Epigenetic and inflammatory markers in older adults with cancer: A Young International Society of Geriatric Oncology narrative review. J Geriatr Oncol 2024; 15:101655. [PMID: 37931584 PMCID: PMC10841884 DOI: 10.1016/j.jgo.2023.101655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023]
Abstract
The number of adults aged ≥ 65 years with cancer is rapidly increasing. Older adults with cancer are susceptible to treatment-related acute and chronic adverse events, resulting in loss of independence, reduction in physical function, and decreased quality of life. Nevertheless, evidence-based interventions to prevent or treat acute and chronic adverse events in older adults with cancer are limited. Several promising blood-based biomarkers related to inflammation and epigenetic modifications are available to identify older adults with cancer who are at increased risk of accelerated aging and physical, functional, and cognitive impairments caused by the cancer and its treatment. Inflammatory changes and epigenetic modifications can be reversible and targeted by lifestyle changes and interventions. Here we discuss ways in which changes in inflammatory and epigenetic pathways influence the aging process and how these pathways can be targeted by interventions aimed at reducing inflammation and aging-associated biological markers. As the number of older adults with cancer entering survivorship continues to increase, it is becoming progressively more important to understand ways in which the benefit from treatment can be enhanced while reducing the effects of accelerated aging.
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Affiliation(s)
- Nikesha Gilmore
- Department of Surgery, Division of Supportive Care in Cancer, University of Rochester Medical Center, Rochester, NY, USA; James P Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
| | - Kah Poh Loh
- James P Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA; Division of Hematology/Oncology, Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA.
| | - Gabor Liposits
- Department of Oncology, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Academy of Geriatric Cancer Research (AgeCare), Odense, Denmark; Department of Oncology, Regional Hospital Gødstrup, Herning, Denmark.
| | - Sukeshi Patel Arora
- Division of Hematology/Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas, USA.
| | - Paula Vertino
- James P Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA; Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, USA.
| | - Michelle Janelsins
- Department of Surgery, Division of Supportive Care in Cancer, University of Rochester Medical Center, Rochester, NY, USA; James P Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
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6
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Nephew BC, Murgatroyd C, Polcari JJ, Santos HP, Incollingo Rodriguez AC. Increasing the use of functional and multimodal genetic data in social science research. Behav Brain Sci 2023; 46:e223. [PMID: 37695007 DOI: 10.1017/s0140525x2200228x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Genetic studies in the social sciences could be augmented through the additional consideration of functional (transcriptome, methylome, metabolome) and/or multimodal genetic data when attempting to understand the genetics of social phenomena. Understanding the biological pathways linking genetics and the environment will allow scientists to better evaluate the functional importance of polygenic scores.
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Affiliation(s)
- Benjamin C Nephew
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Chris Murgatroyd
- School of Healthcare Science, Manchester Metropolitan University, Manchester, UK
| | - Justin J Polcari
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Hudson P Santos
- Department of Nursing, University of Miami, Coral Gables, FL, USA
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7
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Korous KM, Surachman A, Rogers CR, Cuevas AG. Parental education and epigenetic aging in middle-aged and older adults in the United States: A life course perspective. Soc Sci Med 2023; 333:116173. [PMID: 37595421 PMCID: PMC10530379 DOI: 10.1016/j.socscimed.2023.116173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/20/2023]
Abstract
Epigenetic aging is one plausible mechanism by which socioeconomic status (SES) contributes to disparities in morbidity and mortality. Although the association between SES and epigenetic aging is well documented, the role of parental education into adulthood remains understudied. We examined (1) if parental education was independently associated with epigenetic aging, (2) whether upward educational mobility buffered this association, and (3) if the benefit of parental education was differentiated by race/ethnicity. Secondary data analysis of a subsample (n = 3875) of Non-Hispanic [NH] Black, Hispanic, NH White, and NH other race participants from the Venous Blood Study within Health and Retirement Study were examined. Thirteen clocks based on DNA methylation of cytosine-phosphate-guanine sites were used to calculate epigenetic aging. Participants' education (personal) and their report of their respective parent's education (parental; mother's and/or father's) were included as independent variables; several potential confounders were also included. Direct associations and interactions between parental and personal education were estimated via survey-weighted generalized linear models; marginal means for epigenetic aging were estimated and contrasts were made between the education subcategories. Analyses were also stratified by race/ethnicity. Our results showed that higher parental education was independently associated with slower epigenetic aging among four clocks, whereas higher personal education magnified this association among four different epigenetic clocks. Participants with the lowest parental and personal education had higher marginal means (i.e., accelerated aging) compared to participants with the highest parental and personal education, and there was little evidence of upward mobility. These associations were more frequently observed among NH White participants, whereas fewer were observed for Hispanic and NH Black participants. Overall, our findings support that early-life circumstances may be biologically embedded through epigenetic aging, which may also limit the biological benefits associated with one's own education.
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Affiliation(s)
- Kevin M Korous
- Institute for Health & Equity, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Agus Surachman
- Department of Epidemiology and Biostatistics, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Charles R Rogers
- Institute for Health & Equity, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Adolfo G Cuevas
- Social and Behavioral Sciences Department, School of Global Public Health, New York University, New York, NY, USA.
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8
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van Dongen J, Willemsen G, de Geus EJC, Boomsma DI, Neale MC. Effects of smoking on genome-wide DNA methylation profiles: A study of discordant and concordant monozygotic twin pairs. eLife 2023; 12:e83286. [PMID: 37643467 PMCID: PMC10501767 DOI: 10.7554/elife.83286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 08/08/2023] [Indexed: 08/31/2023] Open
Abstract
Background Smoking-associated DNA methylation levels identified through epigenome-wide association studies (EWASs) are generally ascribed to smoking-reactive mechanisms, but the contribution of a shared genetic predisposition to smoking and DNA methylation levels is typically not accounted for. Methods We exploited a strong within-family design, that is, the discordant monozygotic twin design, to study reactiveness of DNA methylation in blood cells to smoking and reversibility of methylation patterns upon quitting smoking. Illumina HumanMethylation450 BeadChip data were available for 769 monozygotic twin pairs (mean age = 36 years, range = 18-78, 70% female), including pairs discordant or concordant for current or former smoking. Results In pairs discordant for current smoking, 13 differentially methylated CpGs were found between current smoking twins and their genetically identical co-twin who never smoked. Top sites include multiple CpGs in CACNA1D and GNG12, which encode subunits of a calcium voltage-gated channel and G protein, respectively. These proteins interact with the nicotinic acetylcholine receptor, suggesting that methylation levels at these CpGs might be reactive to nicotine exposure. All 13 CpGs have been previously associated with smoking in unrelated individuals and data from monozygotic pairs discordant for former smoking indicated that methylation patterns are to a large extent reversible upon smoking cessation. We further showed that differences in smoking level exposure for monozygotic twins who are both current smokers but differ in the number of cigarettes they smoke are reflected in their DNA methylation profiles. Conclusions In conclusion, by analysing data from monozygotic twins, we robustly demonstrate that DNA methylation level in human blood cells is reactive to cigarette smoking. Funding We acknowledge funding from the National Institute on Drug Abuse grant DA049867, the Netherlands Organization for Scientific Research (NWO): Biobanking and Biomolecular Research Infrastructure (BBMRI-NL, NWO 184.033.111) and the BBRMI-NL-financed BIOS Consortium (NWO 184.021.007), NWO Large Scale infrastructures X-Omics (184.034.019), Genotype/phenotype database for behaviour genetic and genetic epidemiological studies (ZonMw Middelgroot 911-09-032); Netherlands Twin Registry Repository: researching the interplay between genome and environment (NWO-Groot 480-15-001/674); the Avera Institute, Sioux Falls (USA), and the National Institutes of Health (NIH R01 HD042157-01A1, MH081802, Grand Opportunity grants 1RC2 MH089951 and 1RC2 MH089995); epigenetic data were generated at the Human Genomics Facility (HuGe-F) at ErasmusMC Rotterdam. Cotinine assaying was sponsored by the Neuroscience Campus Amsterdam. DIB acknowledges the Royal Netherlands Academy of Science Professor Award (PAH/6635).
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit AmsterdamAmsterdamNetherlands
- Amsterdam Public Health Research InstituteAmsterdamNetherlands
- Amsterdam Reproduction and Development (AR&D) Research InstituteAmsterdamNetherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit AmsterdamAmsterdamNetherlands
- Amsterdam Public Health Research InstituteAmsterdamNetherlands
| | - Eco JC de Geus
- Department of Biological Psychology, Vrije Universiteit AmsterdamAmsterdamNetherlands
- Amsterdam Public Health Research InstituteAmsterdamNetherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit AmsterdamAmsterdamNetherlands
- Amsterdam Public Health Research InstituteAmsterdamNetherlands
- Amsterdam Reproduction and Development (AR&D) Research InstituteAmsterdamNetherlands
| | - Michael C Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmondUnited States
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9
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Noble AJ, Nowak JK, Adams AT, Uhlig HH, Satsangi J. Defining Interactions Between the Genome, Epigenome, and the Environment in Inflammatory Bowel Disease: Progress and Prospects. Gastroenterology 2023; 165:44-60.e2. [PMID: 37062395 DOI: 10.1053/j.gastro.2023.03.238] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 03/08/2023] [Accepted: 03/24/2023] [Indexed: 04/18/2023]
Abstract
Recent advances in our understanding of the pathogenesis of inflammatory bowel disease (IBD) have highlighted the complex interplay between the genome, the epigenome, and the environment. Despite the exciting advances in genomics that have enabled the identification of over 200 susceptibility loci, these only account for a small proportion of the disease variance and the estimated heritability in IBD. It is likely that gene-environment (GxE) interactions contribute to "missing heritability" and these may act through epigenetic mechanisms. Several environmental factors, such as the microbiome, nutrition, and tobacco smoking, induce alterations in the epigenome of children and adults, which may impact disease susceptibility. Other mechanisms for GxE interactions are also directly pertinent in early life. We discuss a model in which environmental factors imprint disease risk in a window of susceptibility during infancy that may contribute to later disease onset, whereas other elements of the exposome act later in life and contribute directly to the pathogenesis and course of the disease. Understanding the mechanisms underlying GxE interactions may provide the basis for new therapeutic targets or preventative strategies for IBD.
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Affiliation(s)
- Alexandra J Noble
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom.
| | - Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Alex T Adams
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom; Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom; Department of Pediatrics, University of Oxford, Oxford, United Kingdom; Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom; Biomedical Research Center, University of Oxford, Oxford, United Kingdom
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10
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Kaushik A, Chaudhary V, Longkumer I, Saraswathy KN, Jain S. Sex-specific variations in global DNA methylation levels with age: a population-based exploratory study from North India. Front Genet 2023; 14:1038529. [PMID: 37255712 PMCID: PMC10225692 DOI: 10.3389/fgene.2023.1038529] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/03/2023] [Indexed: 06/01/2023] Open
Abstract
Purpose: Aging is one of the most important risk factors for a number of human diseases. Epigenetic alterations, including changes in DNA methylation patterns, have been reported to be one of the hallmarks of aging. Being a malleable process, the role of site-specific DNA methylation in aging is being extensively investigated; however, much less attention has been given to alterations in global DNA methylation with aging at the population level. The present study aims to explore overall and sex-specific variations in global DNA methylation patterns with age. Methods: A total of 1,127 adult individuals (792 females) aged 30-75 years belonging to Haryana, North India, were recruited. Socio-demographic data was collected using a pretested interview schedule. Global DNA methylation analysis, of peripheral blood leucocyte (PBL) DNA, was performed using the ELISA-based colorimetric technique. Results: Though the overall correlation analysis revealed a weak inverse trend between global DNA methylation and age, the adjusted regression model showed no significant association between global DNA methylation and age. In age-stratified analysis, global DNA methylation levels were found to be fairly stable until 60 years of age, followed by a decline in the above-60 age group. Further, no significant difference in DNA patterns methylation pattern was observed between males and females. Conclusion: Overall, the study suggests a lack of association between global DNA methylation and age, especially until 60 years of age, and a similar DNA methylation pattern between males and females with respect to age.
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Affiliation(s)
- Anshika Kaushik
- Laboratory of Molecular and Biochemical Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | - Vineet Chaudhary
- Laboratory of Molecular and Biochemical Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | - Imnameren Longkumer
- Laboratory of Molecular and Biochemical Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | | | - Sonal Jain
- Laboratory of Molecular and Biochemical Anthropology, Department of Anthropology, University of Delhi, Delhi, India
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11
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O'Shea DM, Alaimo H, Davis JD, Galvin JE, Tremont G. A comparison of cognitive performances based on differing rates of DNA methylation GrimAge acceleration among older men and women. Neurobiol Aging 2023; 123:83-91. [PMID: 36641830 DOI: 10.1016/j.neurobiolaging.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/02/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022]
Abstract
Cognitive heterogeneity increases with age rendering sex differences difficult to identify. Given established sex differences in biological aging, we examined whether comparisons of men and women on neuropsychological test performances differed as a function of age rate. Data were obtained from 1921 adults enrolled in the 2016 wave of the Health and Retirement Study. The residual from regressing the DNA methylation GrimAge clock on chronological age was used as the measure of aging rate. Slow and fast age rates were predefined as 1 standard deviation below or above the sex-specific mean rates, respectively. ANCOVAs were used to test group differences in test performances. Pairwise comparisons revealed that slow aging men outperformed fast aging women (and vice versa) on measures of executive function/speed, visual memory and semantic fluency; however, when groups were matched by aging rates, no significant differences remained. In contrast, women, regardless of their aging rates, education or depressive symptoms maintained their advantage on verbal learning and memory. Implications for research on sex differences in cognitive aging are discussed.
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Affiliation(s)
- Deirdre M O'Shea
- Department of Psychiatry & Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA; Rhode Island Hospital, Providence, RI, USA; Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Boca Raton, FL, USA.
| | | | - Jennifer D Davis
- Department of Psychiatry & Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA; Rhode Island Hospital, Providence, RI, USA
| | - James E Galvin
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Boca Raton, FL, USA
| | - Geoffrey Tremont
- Department of Psychiatry & Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA; Rhode Island Hospital, Providence, RI, USA
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12
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Meijer M, Franke B, Sandi C, Klein M. Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis. Neurosci Biobehav Rev 2023; 145:104997. [PMID: 36566803 DOI: 10.1016/j.neubiorev.2022.104997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/24/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide association studies (EWAS) for externalizing behaviours have been limited in sample size, and, therefore, candidate genes and biomarkers with robust evidence are still lacking. We 1) performed a systematic literature review of EWAS of attention-deficit/hyperactivity disorder (ADHD)- and aggression-related behaviours conducted in peripheral tissue and cord blood and 2) combined the most strongly associated DNAm sites observed in individual studies (p < 10-3) to identify candidate genes and biological systems for ADHD and aggressive behaviours. We observed enrichment for neuronal processes and neuronal cell marker genes for ADHD. Astrocyte and granulocytes cell markers among genes annotated to DNAm sites were relevant for both ADHD and aggression-related behaviours. Only 1 % of the most significant epigenetic findings for ADHD/ADHD symptoms were likely to be directly explained by genetic factors involved in ADHD. Finally, we discuss how the field would greatly benefit from larger sample sizes and harmonization of assessment instruments.
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Affiliation(s)
- Mandy Meijer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carmen Sandi
- Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marieke Klein
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92093, USA.
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13
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Gao C, Amador C, Walker RM, Campbell A, Madden RA, Adams MJ, Bai X, Liu Y, Li M, Hayward C, Porteous DJ, Shen X, Evans KL, Haley CS, McIntosh AM, Navarro P, Zeng Y. Phenome-wide analysis identifies parent-of-origin effects on the human methylome associated with changes in the rate of aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524653. [PMID: 36711749 PMCID: PMC9882261 DOI: 10.1101/2023.01.18.524653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Variation in the rate at which humans age may be rooted in early life events acting through genomic regions that are influenced by such events and subsequently are related to health phenotypes in later life. The parent-of-origin-effect (POE)-regulated methylome includes regions either enriched for genetically controlled imprinting effects (the typical type of POE) or atypical POE introduced by environmental effects associated with parents. This part of the methylome is heavily influenced by early life events, making it a potential route connecting early environmental exposures, the epigenome and the rate of aging. Here, we aim to test the association of POE-influenced methylation of CpG dinucleotides (POE-CpG sites) with early and later environmental exposures and subsequently with health-related phenotypes and adult aging phenotypes. We do this by performing phenome-wide association analyses of the POE-influenced methylome using a large family-based population cohort (GS:SFHS, Ndiscovery=5,087, Nreplication=4,450). At the single CpG level, 92 associations of POE-CpGs with phenotypic variation were identified and replicated. Most of the associations were contributed by POE-CpGs belonging to the atypical class and the most strongly enriched associations were with aging (DNAmTL acceleration), intelligence and parental (maternal) smoking exposure phenotypes. We further found that a proportion of the atypical-POE-CpGs formed co-methylation networks (modules) which are associated with these phenotypes, with one of the aging-associated modules displaying increased internal module connectivity (strength of methylation correlation across constituent CpGs) with age. Atypical POE-CpGs also displayed high levels of methylation heterogeneity and epigenetic drift (i.e. information loss with age) and a strong correlation with CpGs contained within epigenetic clocks. These results identified associations between the atypical-POE-influenced methylome and aging and provided new evidence for the "early development of origin" hypothesis for aging in humans.
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Affiliation(s)
- Chenhao Gao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rosie M. Walker
- Centre for Clinical Brain Sciences, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- School of Psychology, University of Exeter, Perry Road, Exeter, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rebecca A Madden
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Mark J. Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Xiaomeng Bai
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Ying Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xueyi Shen
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Chris S. Haley
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Andrew M. McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Yanni Zeng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
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14
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Gunasekara CJ, MacKay H, Scott CA, Li S, Laritsky E, Baker MS, Grimm SL, Jun G, Li Y, Chen R, Wiemels JL, Coarfa C, Waterland RA. Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control. Genome Biol 2023; 24:2. [PMID: 36631879 PMCID: PMC9835319 DOI: 10.1186/s13059-022-02827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/01/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL at human genomic regions selected for interindividual variation in CpG methylation, which we call correlated regions of systemic interindividual variation (CoRSIVs). These can be assayed in blood DNA and do not reflect interindividual variation in cellular composition. RESULTS We use target-capture bisulfite sequencing to assess DNA methylation at 4086 CoRSIVs in multiple tissues from each of 188 donors in the NIH Gene-Tissue Expression (GTEx) program. At CoRSIVs, DNA methylation in peripheral blood correlates with methylation and gene expression in internal organs. We also discover unprecedented mQTL at these regions. Genetic influences on CoRSIV methylation are extremely strong (median R2=0.76), cumulatively comprising over 70-fold more human mQTL than detected in the most powerful previous study. Moreover, mQTL beta coefficients at CoRSIVs are highly skewed (i.e., the major allele predicts higher methylation). Both surprising findings are independently validated in a cohort of 47 non-GTEx individuals. Genomic regions flanking CoRSIVs show long-range enrichments for LINE-1 and LTR transposable elements; the skewed beta coefficients may therefore reflect evolutionary selection of genetic variants that promote their methylation and silencing. Analyses of GWAS summary statistics show that mQTL polymorphisms at CoRSIVs are associated with metabolic and other classes of disease. CONCLUSIONS A focus on systemic interindividual epigenetic variants, clearly enhanced in mQTL content, should likewise benefit studies attempting to link human epigenetic variation to the risk of disease.
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Affiliation(s)
- Chathura J. Gunasekara
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Harry MacKay
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - C. Anthony Scott
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Shaobo Li
- grid.42505.360000 0001 2156 6853Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Eleonora Laritsky
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Maria S. Baker
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Sandra L. Grimm
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Goo Jun
- grid.267308.80000 0000 9206 2401Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Yumei Li
- grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Rui Chen
- grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Joseph L. Wiemels
- grid.42505.360000 0001 2156 6853Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Cristian Coarfa
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX USA
| | - Robert A. Waterland
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
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15
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Noro F, Santonastaso F, Marotta A, Bonaccio M, Orlandi S, Tirozzi A, Costanzo S, De Curtis A, Gianfagna F, Di Castelnuovo A, Brighenti F, Cerletti C, Donati MB, de Gaetano G, Iacoviello L, Gialluisi A, Izzi B, de Gaetano G, Donati MB, Bonaccio M, Bonanni A, Cerletti C, Costanzo S, De Curtis A, Di Castelnuovo A, Gialluisi A, Gianfagna F, Persichillo M, Di Prospero T, Vermylen J, Pegoraro R, Spagnolo A, Assanelli D, Rago L, Costanzo S, Olivieri M, Panzera T, Di Castelnuovo A, Bonaccio M, Costanzo S, Esposito S, Gialluisi A, Gianfagna F, Orlandi S, Ruggiero E, Tirozzi A, De Curtis A, Magnacca S, Noro F, Tirozzi A, Persichillo M, Bracone F, Panzera T, Bonanni A. Association of nutritional glycaemic indices with global DNA methylation patterns: results from the Moli-sani cohort. Clin Epigenetics 2022; 14:189. [PMID: 36578055 PMCID: PMC9798643 DOI: 10.1186/s13148-022-01407-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/13/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND High dietary glycaemic index (GI) and load (GL) have been associated with increased risk of various cardiometabolic conditions. Among the molecular potential mechanisms underlying this relationship, DNA methylation has been studied, but a direct link between high GI and/or GL of diet and global DNA methylation levels has not been proved yet. We analyzed the associations between GI and GL and global DNA methylation patterns within an Italian population. RESULTS Genomic DNA methylation (5mC) and hydroxymethylation (5hmC) levels were measured in 1080 buffy coat samples from participants of the Moli-sani study (mean(SD) = 54.9(11.5) years; 52% women) via ELISA. A 188-item Food Frequency Questionnaire was used to assess food intake and dietary GI and GL for each participant were calculated. Multiple linear regressions were used to investigate the associations between dietary GI and GL and global 5mC and 5hmC levels, as well as the proportion of effect explained by metabolic and inflammatory markers. We found negative associations of GI with both 5mC (β (SE) = - 0.073 (0.027), p = 0.007) and 5hmC (- 0.084 (0.030), p = 0.006), and of GL with 5mC (- 0.14 (0.060), p = 0.014). Circulating biomarkers did not explain the above-mentioned associations. Gender interaction analyses revealed a significant association of the gender-x-GL interaction with 5mC levels, with men showing an inverse association three times as negative as in women (interaction β (SE) = - 0.16 (0.06), p = 0.005). CONCLUSIONS Our findings suggest that global DNA methylation and hydroxymethylation patterns represent a biomarker of carbohydrate intake. Based on the differential association of GL with 5mC between men and women, further gender-based separate approaches are warranted.
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Affiliation(s)
- Fabrizia Noro
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Federica Santonastaso
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy ,grid.510779.d0000 0004 9414 6915Present Address: Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy ,grid.4708.b0000 0004 1757 2822Present Address: European School of Molecular Medicine, University of Milan, 20122 Milan, Italy
| | - Annalisa Marotta
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy ,grid.412451.70000 0001 2181 4941Present Address: Center of Predictive Molecular Medicine, Center for Excellence on Ageing and Translational Medicine (CAST), University of Chieti-Pescara, Chieti, Italy
| | - Marialaura Bonaccio
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Sabatino Orlandi
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Alfonsina Tirozzi
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Simona Costanzo
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Amalia De Curtis
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Francesco Gianfagna
- grid.18147.3b0000000121724807EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy ,grid.477084.80000 0004 1787 3414Mediterranea Cardiocentro, Naples, Italy
| | | | - Furio Brighenti
- grid.10383.390000 0004 1758 0937Department of Food and Drug, University of Parma, Parma, Italy
| | - Chiara Cerletti
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Maria Benedetta Donati
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Giovanni de Gaetano
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Licia Iacoviello
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy ,grid.18147.3b0000000121724807EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Alessandro Gialluisi
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy ,grid.18147.3b0000000121724807EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Benedetta Izzi
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
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16
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Rajaprakash M, Dean LT, Palmore M, Johnson SB, Kaufman J, Fallin DM, Ladd-Acosta C. DNA methylation signatures as biomarkers of socioeconomic position. ENVIRONMENTAL EPIGENETICS 2022; 9:dvac027. [PMID: 36694711 PMCID: PMC9869656 DOI: 10.1093/eep/dvac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 11/22/2022] [Accepted: 12/13/2022] [Indexed: 06/12/2023]
Abstract
This review article provides a framework for the use of deoxyribonucleic acid (DNA) methylation (DNAm) biomarkers to study the biological embedding of socioeconomic position (SEP) and summarizes the latest developments in the area. It presents the emerging literature showing associations between individual- and neighborhood-level SEP exposures and DNAm across the life course. In contrast to questionnaire-based methods of assessing SEP, we suggest that DNAm biomarkers may offer an accessible metric to study questions about SEP and health outcomes, acting as a personal dosimeter of exposure. However, further work remains in standardizing SEP measures across studies and evaluating consistency across domains, tissue types, and time periods. Meta-analyses of epigenetic associations with SEP are offered as one approach to confirm the replication of DNAm loci across studies. The development of DNAm biomarkers of SEP would provide a method for examining its impact on health outcomes in a more robust way, increasing the rigor of epidemiological studies.
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Affiliation(s)
- Meghna Rajaprakash
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Lorraine T Dean
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Meredith Palmore
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sara B Johnson
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Joan Kaufman
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Daniele M Fallin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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17
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Zhang X, Ammous F, Lin L, Ratliff SM, Ware EB, Faul JD, Zhao W, Kardia SLR, Smith JA. The Interplay of Epigenetic, Genetic, and Traditional Risk Factors on Blood Pressure: Findings from the Health and Retirement Study. Genes (Basel) 2022; 13:1959. [PMID: 36360196 PMCID: PMC9689874 DOI: 10.3390/genes13111959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 01/21/2023] Open
Abstract
The epigenome likely interacts with traditional and genetic risk factors to influence blood pressure. We evaluated whether 13 previously reported DNA methylation sites (CpGs) are associated with systolic (SBP) or diastolic (DBP) blood pressure, both individually and aggregated into methylation risk scores (MRS), in 3070 participants (including 437 African ancestry (AA) and 2021 European ancestry (EA), mean age = 70.5 years) from the Health and Retirement Study. Nine CpGs were at least nominally associated with SBP and/or DBP after adjusting for traditional hypertension risk factors (p < 0.05). MRSSBP was positively associated with SBP in the full sample (β = 1.7 mmHg per 1 standard deviation in MRSSBP; p = 2.7 × 10-5) and in EA (β = 1.6; p = 0.001), and MRSDBP with DBP in the full sample (β = 1.1; p = 1.8 × 10-6), EA (β = 1.1; p = 7.2 × 10-5), and AA (β = 1.4; p = 0.03). The MRS and BP-genetic risk scores were independently associated with blood pressure in EA. The effects of both MRSs were weaker with increased age (pinteraction < 0.01), and the effect of MRSDBP was higher among individuals with at least some college education (pinteraction = 0.02). In AA, increasing MRSSBP was associated with higher SBP in females only (pinteraction = 0.01). Our work shows that MRS is a potential biomarker of blood pressure that may be modified by traditional hypertension risk factors.
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Affiliation(s)
- Xinman Zhang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lisha Lin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erin B. Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
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18
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Fransquet PD, Hjort L, Rushiti F, Wang S, Krasniqi SP, Çarkaxhiu SI, Arifaj D, Xhemaili VD, Salihu M, Leku NA, Ryan J. DNA methylation in blood cells is associated with cortisol levels in offspring of mothers who had prenatal post‐traumatic stress disorder. Stress Health 2022; 38:755-766. [PMID: 35119793 PMCID: PMC9790331 DOI: 10.1002/smi.3131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 12/30/2022]
Abstract
Maternal stress during pregnancy is associated with differential DNA methylation in offspring and disrupted cortisol secretion. This study aimed to determine methylation signatures of cortisol levels in children, and whether associations differ based on maternal post-traumatic stress disorder (PTSD). Blood epigenome-wide methylation and fasting cortisol levels were measured in 118 offspring of mothers recruited from the Kosovo Rehabilitation Centre for Torture Victims. Mothers underwent clinically administered assessment for PTSD using Diagnostic and Statistical Manual of Mental Disorders. Correlations between offspring methylation and cortisol levels were examined using epigenome-wide analysis, adjusting for covariates. Subsequent analysis focussed on a priori selected genes involved in the hypothalamic-pituitary-adrenal (HPA) axis stress signalling. Methylation at four sites were correlated with cortisol levels (cg15321696, r = -0.33, cg18105800, r = +0.33, cg00986889, r = -0.25, and cg15920527, r = -0.27). In adjusted multivariable regression, when stratifying based on prenatal PTSD status, significant associations were only found for children born to mothers with prenatal PTSD (p < 0.001). Several sites within HPA axis genes were also associated with cortisol levels in the maternal PTSD group specifically. There is evidence that methylation is associated with cortisol levels, particularly in offspring born to mothers with prenatal PTSD. However, larger studies need to be carried out to independently validate these findings.
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Affiliation(s)
- Peter Daniel Fransquet
- School of Public Health and Preventive MedicineBiological Neuropsychiatry and Dementia UnitMonash UniversityMelbourneVictoriaAustralia
| | - Line Hjort
- Department of ObstetricsCenter for Pregnant Women with DiabetesRigshospitaletCopenhagenDenmark,Novo Nordisk Foundation Center for Basic Metabolic ResearchMetabolic Epigenetics GroupFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Feride Rushiti
- Kosovo Rehabilitation Center for Torture VictimsPristinaAlbania
| | - Shr‐Jie Wang
- Danish Institute Against Torture (DIGNITY)CopenhagenDenmark
| | | | | | - Dafina Arifaj
- Kosovo Rehabilitation Center for Torture VictimsPristinaAlbania
| | | | - Mimoza Salihu
- Kosovo Rehabilitation Center for Torture VictimsPristinaAlbania
| | | | - Joanne Ryan
- School of Public Health and Preventive MedicineBiological Neuropsychiatry and Dementia UnitMonash UniversityMelbourneVictoriaAustralia
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19
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DNA Methylation Profiles of the DRD2 and NR3C1 Genes in Patients with Recent-Onset Psychosis. DISEASE MARKERS 2022; 2022:2172564. [PMID: 35968502 PMCID: PMC9365600 DOI: 10.1155/2022/2172564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/25/2022] [Accepted: 07/14/2022] [Indexed: 01/21/2023]
Abstract
Objectives Dopamine receptor D2 gene (DRD2) and glucocorticoid receptor gene (NR3C1) are implicated in the development of psychosis. We investigated methylation levels of DRD2 and NR3C1 in peripheral blood of patients with recent-onset (RO) psychosis using bisulfite pyrosequencing as well as its association with childhood trauma and rumination. Methods In all, 51 individuals with RO psychosis and 47 healthy controls were recruited. DNA methylation levels in the targeted regions of two genes were analyzed and compared. Childhood trauma and rumination were evaluated using the Early Trauma Inventory Self-Report Short Form (ETI-SF) and Brooding Scale (BS), respectively. Correlations between the scores of the ETI-SF and BS and methylation levels were explored. Results For DRD2, we found no significant differences between groups in terms of methylation level or association with childhood trauma or rumination. For NR3C1, we found a trend level significance for average value of all CpG sites and significant hypermethylation or hypomethylation at specific sites. There was also a significant positive correlation between the methylation level at the CpG8 site of NR3C1 exon 1F and negative symptom subscale score of the PANSS (PANSS-N). Conclusion Epigenetic alterations of NR3C1 are associated with the pathophysiology of psychosis. Further epigenetic studies will elucidate the molecular mechanisms underpinning the pathophysiology of psychosis.
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20
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Thomas SV, Salim S, Jacob NS, Jose M, Salini RA, Selvaraj S, Gomez TS, Sreedharan H, Jeemon P. Language, intelligence, and educational outcomes of adolescents with antenatal exposure to antiseizure medications: Prospective data from the Kerala Registry of epilepsy and pregnancy. Seizure 2022; 100:76-81. [DOI: 10.1016/j.seizure.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 11/15/2022] Open
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21
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Eckhardt CM, Wu H, Prada D, Vokonas PS, Sparrow D, Hou L, Schwartz J, Baccarelli AA. Predicting risk of lung function impairment and all-cause mortality using a DNA methylation-based classifier of tobacco smoke exposure. Respir Med 2022; 200:106896. [PMID: 35716602 PMCID: PMC10560590 DOI: 10.1016/j.rmed.2022.106896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/09/2022] [Accepted: 05/30/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND The Epigenetic Smoking Status Estimator (EpiSmokEr) predicts smoking phenotypes based on DNA methylation at 121 CpG sites. OBJECTIVE Evaluate associations of EpiSmokEr-predicted versus self-reported smoking phenotypes with lung function and all-cause mortality in a cohort of older adults. METHODS The prospective Normative Aging Study collected DNA methylation measurements from 1999 to 2012 with follow-up through 2016. The R package EpiSmokEr derived predicted smoking phenotypes based on DNA methylation levels assayed by the Illumina HumanMethylation450 Beadchip. Spirometry was collected every 3-5 years. Airflow limitation was defined as forced expiratory volume in 1 s/forced vital capacity <0.7. Vital status was monitored through periodic mailings. RESULTS Among 784 participants contributing 5414 person-years of follow-up, the EpiSmokEr-predicted smoking phenotypes matched the self-reported phenotypes for 228 (97%) never smokers and 22 (71%) current smokers. In contrast, EpiSmokEr classified 407 (79%) self-reported former smokers as never smokers. Nonetheless, the EpiSmokEr-predicted former smoking phenotype was more strongly associated with incident airflow limitation (hazard ratio [HR] = 3.15, 95% confidence interval [CI] = 1.50-6.59) and mortality (HR = 2.11, 95% CI = 1.56-2.85) compared to the self-reported former smoking phenotype (airflow limitation: HR = 2.21, 95% CI = 1.13-4.33; mortality: HR = 1.08, 95% CI = 0.86-1.36). Risk of airflow limitation and death did not differ among self-reported never smokers and former smokers who were classified as never smokers. The discriminative accuracy of EpiSmokEr-predicted phenotypes for incident airflow limitation and mortality was improved compared to self-reported phenotypes. CONCLUSIONS The DNA methylation-based EpiSmokEr classifier may be a useful surrogate of smoking-induced lung damage and may identify former smokers most at risk of adverse smoking-related health effects.
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Affiliation(s)
- Christina M Eckhardt
- Columbia University Irving Medical Center, Division of Pulmonary, Allergy and Critical, Care Medicine, Department of Medicine, New York, NY, USA.
| | - Haotian Wu
- Columbia University Mailman School of Public Health, Environmental Health Sciences, Department, New York, NY, USA
| | - Diddier Prada
- Columbia University Mailman School of Public Health, Environmental Health Sciences, Department, New York, NY, USA; Instituto Nacional de Cancerología, México City, Mexico
| | - Pantel S Vokonas
- Boston University School of Medicine, VA Normative Aging Study, VA, Boston, USA; Healthcare System and Department of Medicine, Boston, MA, USA
| | - David Sparrow
- Boston University School of Medicine, VA Normative Aging Study, VA, Boston, USA; Healthcare System and Department of Medicine, Boston, MA, USA
| | - Lifang Hou
- Northwestern Feinberg School of Medicine, Department of Preventive Medicine, Chicago, IL, USA
| | - Joel Schwartz
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Cambridge, MA, USA
| | - Andrea A Baccarelli
- Columbia University Mailman School of Public Health, Environmental Health Sciences, Department, New York, NY, USA
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22
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Barbu MC, Amador C, Kwong ASF, Shen X, Adams MJ, Howard DM, Walker RM, Morris SW, Min JL, Liu C, van Dongen J, Ghanbari M, Relton C, Porteous DJ, Campbell A, Evans KL, Whalley HC, McIntosh AM. Complex trait methylation scores in the prediction of major depressive disorder. EBioMedicine 2022; 79:104000. [PMID: 35490552 PMCID: PMC9062752 DOI: 10.1016/j.ebiom.2022.104000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND DNA methylation (DNAm) is associated with time-varying environmental factors that contribute to major depressive disorder (MDD) risk. We sought to test whether DNAm signatures of lifestyle and biochemical factors were associated with MDD to reveal dynamic biomarkers of MDD risk that may be amenable to lifestyle interventions. METHODS Here, we calculated methylation scores (MS) at multiple p-value thresholds for lifestyle (BMI, smoking, alcohol consumption, and educational attainment) and biochemical (high-density lipoprotein (HDL) and total cholesterol) factors in Generation Scotland (GS) (N=9,502) and in a replication cohort (ALSPACadults, N=565), using CpG sites reported in previous well-powered methylome-wide association studies. We also compared their predictive accuracy for MDD to a MDD MS in an independent GS sub-sample (N=4,432). FINDINGS Each trait MS was significantly associated with its corresponding phenotype in GS (βrange=0.089-1.457) and in ALSPAC (βrange=0.078-2.533). Each MS was also significantly associated with MDD before and after adjustment for its corresponding phenotype in GS (βrange=0.053-0.145). After accounting for relevant lifestyle factors, MS for educational attainment (β=0.094) and alcohol consumption (MSp-value<0.01-0.5; βrange=-0.069-0.083) remained significantly associated with MDD in GS. Smoking (AUC=0.569) and educational attainment (AUC=0.585) MSs could discriminate MDD from controls better than the MDD MS (AUC=0.553) in the independent GS sub-sample. Analyses implicating MDD did not replicate across ALSPAC, although the direction of effect was consistent for all traits when adjusting for the MS corresponding phenotypes. INTERPRETATION We showed that lifestyle and biochemical MS were associated with MDD before and after adjustment for their corresponding phenotypes (pnominal<0.05), but not when smoking, alcohol consumption, and BMI were also included as covariates. MDD results did not replicate in the smaller, female-only independent ALSPAC cohort (NALSPAC=565; NGS=9,502), potentially due to demographic differences or low statistical power, but effect sizes were consistent with the direction reported in GS. DNAm scores for modifiable MDD risk factors may contribute to disease vulnerability and, in some cases, explain additional variance to their observed phenotypes. FUNDING Wellcome Trust.
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Affiliation(s)
- Miruna C Barbu
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh EH10 5HF, United Kingdom.
| | - Carmen Amador
- MRC Human Genetics Unit, The Institute of Genetics and Cancer, The University of Edinburgh, United Kingdom
| | - Alex S F Kwong
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh EH10 5HF, United Kingdom
| | - Xueyi Shen
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh EH10 5HF, United Kingdom
| | - Mark J Adams
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh EH10 5HF, United Kingdom
| | - David M Howard
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh EH10 5HF, United Kingdom; Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, United Kingdom
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, The Institute of Genetics and Cancer, The University of Edinburgh, United Kingdom
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, The Institute of Genetics and Cancer, The University of Edinburgh, United Kingdom
| | - Josine L Min
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom
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- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; The Framingham Heart Study, Framingham, MA, USA
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, the Netherlands
| | - Caroline Relton
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, The Institute of Genetics and Cancer, The University of Edinburgh, United Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, The Institute of Genetics and Cancer, The University of Edinburgh, United Kingdom
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, The Institute of Genetics and Cancer, The University of Edinburgh, United Kingdom
| | - Heather C Whalley
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh EH10 5HF, United Kingdom
| | - Andrew M McIntosh
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh EH10 5HF, United Kingdom
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23
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Song N, Sim JA, Dong Q, Zheng Y, Hou L, Li Z, Hsu CW, Pan H, Mulder H, Easton J, Walker E, Neale G, Wilson CL, Ness KK, Krull KR, Srivastava DK, Yasui Y, Zhang J, Hudson MM, Robison LL, Huang IC, Wang Z. Blood DNA methylation signatures are associated with social determinants of health among survivors of childhood cancer. Epigenetics 2022; 17:1389-1403. [PMID: 35109748 PMCID: PMC9586655 DOI: 10.1080/15592294.2022.2030883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Social epigenomics is an emerging field in which social scientist collaborate with computational biologists, especially epigeneticists, to address the underlying pathway for biological embedding of life experiences. This social epigenomics study included long-term childhood cancer survivors enrolled in the St. Jude Lifetime Cohort. DNA methylation (DNAm) data were generated using the Illumina EPIC BeadChip, and three social determinants of health (SDOH) factors were assessed: self-reported educational attainment, personal income, and an area deprivation index based on census track data. An epigenome-wide association study (EWAS) was performed to evaluate the relation between DNAm at each 5’-cytosine-phosphate-guanine-3’ (CpG) site and each SDOH factor based on multivariable linear regression models stratified by ancestry (European ancestry, n = 1,618; African ancestry, n = 258). EWAS among survivors of European ancestry identified 130 epigenome-wide significant SDOH–CpG associations (P < 9 × 10−8), 25 of which were validated in survivors of African ancestry (P < 0.05). Thirteen CpGs were associated with all three SDOH factors and resided at pleiotropic loci in cigarette smoking–related genes (e.g., CLDND1 and CPOX). After accounting for smoking and body mass index, these associations remained significant with attenuated effect sizes. Seven of 13 CpGs were associated with gene expression level based on 57 subsamples with blood RNA sequencing data available. In conclusion, DNAm signatures, many resembling the effect of tobacco use, were associated with SDOH factors among survivors of childhood cancer, thereby suggesting that biologically distal SDOH factors influence health behaviours or related factors, the epigenome, and subsequently survivors’ health.
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Affiliation(s)
- Nan Song
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy, College of Pharmacy, Chungbuk National University, Cheongju, Chungcheongbuk-do, Korea
| | - Jin-Ah Sim
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,School of Ai Convergence, Hallym University, Chuncheon, Gangwon-do, Korea
| | - Qian Dong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Zhenghong Li
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chia-Wei Hsu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Haitao Pan
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Mulder
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Easton
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Emily Walker
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,St. Jude Children's Research Hospital, Hartwell Center, Memphis, TN, USA
| | - Geoffrey Neale
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,St. Jude Children's Research Hospital, Hartwell Center, Memphis, TN, USA
| | - Carmen L Wilson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kevin R Krull
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Psychology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deo Kumar Srivastava
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Melissa M Hudson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - I-Chan Huang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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24
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Gohar J, Do WL, Miller-Kleinhenz J, Conneely K, Krishnamurti U, D'Angelo O, Gogineni K, Torres M, Gabram-Mendola S, McCullough LE. Neighborhood characteristics and breast tumor methylation: using epigenomics to explore cancer outcome disparities. Breast Cancer Res Treat 2022; 191:653-663. [PMID: 34978015 DOI: 10.1007/s10549-021-06430-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/15/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Social exposures may drive epigenetic alterations that affect racial disparities in breast cancer outcomes. This study examined the association between neighborhood-level factors and DNA methylation in non-Hispanic Black and White women diagnosed with breast cancer. METHODS Genome-wide DNA methylation was measured using the EPIC array in the tumor tissue of 96 women. Linear regression models were used to examine the association between nine neighborhood-level factors and methylation, regressing β values for each cytosine-phosphate guanine dinucleotide (CpG) site on neighborhood-level factors while adjusting for covariates. Neighborhood data were obtained from the Opportunity Atlas. We used a false discovery rate (FDR) threshold < 0.05, and for CpGs below this threshold, we examined interactions with race. We employed multivariable Cox proportional-hazards models to estimate whether aberrant methylation was associated with all-cause mortality. RESULTS 26 of the CpG sites were associated with job density or college education (FDR < 0.05). Further exploration of these 26 CpG sites revealed no interactions by race, but a single probe in TMEM204 was associated with all-cause mortality. CONCLUSION We identified novel associations between neighborhood-level factors and the breast tumor DNA methylome. Our data are the first to show that dysregulation in neighborhood associated CpG sites may be associated with all-cause mortality. Neighborhood-level factors may contribute to differential tumor methylation in genes related to tumor progression and metastasis. This contributes to the increasing body of evidence that area-level factors (such as neighborhood characteristics) may play an important role in cancer disparities through modulation of the breast tumor epigenome.
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Affiliation(s)
- Jazib Gohar
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA
| | - Whitney L Do
- Department of Global Health, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA
| | - Jasmine Miller-Kleinhenz
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA
| | - Karen Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Uma Krishnamurti
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Olivia D'Angelo
- Department of Surgery, Jackson Memorial Hospital/University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Keerthi Gogineni
- Department of Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Mylin Torres
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | | | - Lauren E McCullough
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA.
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25
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Chen GK, Yan Q, Paul KC, Kusters CD, Folle AD, Furlong M, Keener A, Bronstein J, Horvath S, Ritz B. Stochastic Epigenetic Mutations Influence Parkinson's Disease Risk, Progression, and Mortality. JOURNAL OF PARKINSON'S DISEASE 2022; 12:545-556. [PMID: 34842194 PMCID: PMC9076404 DOI: 10.3233/jpd-212834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Stochastic epigenetic mutations (SEM) reflect a deviation from normal site-specific methylation patterns. Epigenetic mutation load (EML) captures the accumulation of SEMs across an individual's genome and may reflect dysfunction of the epigenetic maintenance system in response to epigenetic challenges. OBJECTIVE We investigate whether EML is associated with PD risk and time to events (i.e., death and motor symptom decline). METHODS We employed logistic regression and Cox proportional hazards regression to assess the association between EML and several outcomes. Our analyses are based on 568 PD patients and 238 controls from the Parkinson's disease, Environment and Genes (PEG) study, for whom blood-based methylation data was available. RESULTS We found an association for PD onset and EML in all genes (OR = 1.90; 95%CI 1.52-2.37) and PD-related genes (OR = 1.87; 95%CI 1.50-2.32). EML was also associated with time to a minimum score of 35 points on the motor UPDRS exam (OR = 1.28; 95%CI 1.06-1.56) and time to death (OR = 1.29, 95%CI 1.11-1.49). An analysis of PD related genes only revealed five intragenic hotspots of high SEM density associated with PD risk. CONCLUSION Our findings suggest an enrichment of methylation dysregulation in PD patients in general and specifically in five PD related genes. EML may also be associated with time to death and motor symptom progression in PD patients.
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Affiliation(s)
| | - Qi Yan
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Kimberly C. Paul
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Cynthia D.J. Kusters
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Aline Duarte Folle
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Melissa Furlong
- Department of Community, Environment and Policy, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, AZ, USA
| | - Adrienne Keener
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jeff Bronstein
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
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26
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Cerutti J, Lussier AA, Zhu Y, Liu J, Dunn EC. Associations between indicators of socioeconomic position and DNA methylation: a scoping review. Clin Epigenetics 2021; 13:221. [PMID: 34906220 PMCID: PMC8672601 DOI: 10.1186/s13148-021-01189-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Socioeconomic position (SEP) is a major determinant of health across the life course. Yet, little is known about the biological mechanisms explaining this relationship. One possibility widely pursued in the scientific literature is that SEP becomes biologically embedded through epigenetic processes such as DNA methylation (DNAm), wherein the socioeconomic environment causes no alteration in the DNA sequence but modifies gene activity in ways that shape health. METHODS To understand the evidence supporting a potential SEP-DNAm link, we performed a scoping review of published empirical findings on the association between SEP assessed from prenatal development to adulthood and DNAm measured across the life course, with an emphasis on exploring how the developmental timing, duration, and type of SEP exposure influenced DNAm. RESULTS Across the 37 identified studies, we found that: (1) SEP-related DNAm signatures varied across the timing, duration, and type of SEP indicator; (2) however, longitudinal studies examining repeated SEP and DNAm measures are generally lacking; and (3) prior studies are conceptually and methodologically diverse, limiting the interpretability of findings across studies with respect to these three SEP features. CONCLUSIONS Given the complex relationship between SEP and DNAm across the lifespan, these findings underscore the importance of analyzing SEP features, including timing, duration, and type. To guide future research, we highlight additional research gaps and propose four recommendations to further unravel the relationship between SEP and DNAm.
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Affiliation(s)
- Janine Cerutti
- Department of Pscyhology, University of Vermont, 2 Colchester Ave, Burlington, VT, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
| | - Alexandre A Lussier
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yiwen Zhu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jiaxuan Liu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Erin C Dunn
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA.
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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27
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Gomez-Verjan JC, Esparza-Aguilar M, Martín-Martín V, Salazar-Perez C, Cadena-Trejo C, Gutierrez-Robledo LM, Martínez-Magaña JJ, Nicolini H, Arroyo P. Years of Schooling Could Reduce Epigenetic Aging: A Study of a Mexican Cohort. Genes (Basel) 2021; 12:1408. [PMID: 34573390 PMCID: PMC8469534 DOI: 10.3390/genes12091408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 12/03/2022] Open
Abstract
Adverse conditions in early life, including environmental, biological and social influences, are risk factors for ill-health during aging and the onset of age-related disorders. In this context, the recent field of social epigenetics offers a valuable method for establishing the relationships among them However, current clinical studies on environmental changes and lifespan disorders are limited. In this sense, the Tlaltizapan (Mexico) cohort, who 52 years ago was exposed to infant malnutrition, low income and poor hygiene conditions, represents a vital source for exploring such factors. Therefore, in the present study, 52 years later, we aimed to explore differences in clinical/biochemical/anthropometric and epigenetic (DNA methylation) variables between individuals from such a cohort, in comparison with an urban-raised sample. Interestingly, only cholesterol levels showed significant differences between the cohorts. On the other hand, individuals from the Tlaltizapan cohort with more years of schooling had a lower epigenetic age in the Horvath (p-value = 0.0225) and PhenoAge (p-value = 0.0353) clocks, compared to those with lower-level schooling. Our analysis indicates 12 differentially methylated sites associated with the PI3-Akt signaling pathway and galactose metabolism in individuals with different durations of schooling. In conclusion, our results suggest that longer durations of schooling could promote DNA methylation changes that may reduce epigenetic age; nevertheless, further studies are needed.
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Affiliation(s)
- Juan Carlos Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico City 10200, Mexico; (C.C.-T.); (P.A.)
| | - Marcelino Esparza-Aguilar
- Departamento de Investigación en Epidemiología, Instituto Nacional de Pediatría, Mexico City 04530, Mexico; (M.E.-A.); (C.S.-P.)
| | - Verónica Martín-Martín
- Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City 04530, Mexico;
| | - Cecilia Salazar-Perez
- Departamento de Investigación en Epidemiología, Instituto Nacional de Pediatría, Mexico City 04530, Mexico; (M.E.-A.); (C.S.-P.)
| | - Cinthya Cadena-Trejo
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico City 10200, Mexico; (C.C.-T.); (P.A.)
| | | | - José Jaime Martínez-Magaña
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Mexico City 04809, Mexico; (J.J.M.-M.); (H.N.)
| | - Humberto Nicolini
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Mexico City 04809, Mexico; (J.J.M.-M.); (H.N.)
| | - Pedro Arroyo
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico City 10200, Mexico; (C.C.-T.); (P.A.)
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28
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Tobi EW, Almqvist C, Hedman A, Andolf E, Holte J, Olofsson JI, Wramsby H, Wramsby M, Pershagen G, Heijmans BT, Iliadou AN. DNA methylation differences at birth after conception through ART. Hum Reprod 2021; 36:248-259. [PMID: 33227132 PMCID: PMC7801794 DOI: 10.1093/humrep/deaa253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/21/2020] [Indexed: 12/25/2022] Open
Abstract
STUDY QUESTION Is there a relation between ART and DNA methylation (DNAm) patterns in cord blood, including any differences between IVF and ICSI? SUMMARY ANSWER DNAm at 19 CpGs was associated with conception via ART, with no difference found between IVF and ICSI. WHAT IS KNOWN ALREADY Prior studies on either IVF or ICSI show conflicting outcomes, as both widespread effects on DNAm and highly localized associations have been reported. No study on both IVF and ICSI and genome-wide neonatal DNAm has been performed. STUDY DESIGN, SIZE, DURATION This was a cross-sectional study comprising 87 infants conceived with IVF or ICSI and 70 conceived following medically unassisted conception. The requirement for inclusion in the study was an understanding of the Swedish language and exclusion was the use of donor gametes. PARTICIPANTS/MATERIALS, SETTING, METHODS Participants were from the UppstART study, which was recruited from fertility and reproductive health clinics, and the Born into Life cohort, which is recruited from the larger LifeGene study. We measured DNAm from DNA extracted from cord blood collected at birth using a micro-array (450k array). Group differences in DNAm at individual CpG dinucleotides (CpGs) were determined using robust linear models and post-hoc Tukey’s tests. MAIN RESULTS AND THE ROLE OF CHANCE We found no association of ART conception with global methylation levels, imprinted loci and meta-stable epialleles. In contrast, we identify 19 CpGs at which DNAm was associated with being conceived via ART (effect estimates: 0.5–4.9%, PFDR < 0.05), but no difference was found between IVF and ICSI. The associated CpGs map to genes related to brain function/development or genes connected to the plethora of conditions linked to subfertility, but functional annotation did not point to any likely functional consequences. LIMITATIONS, REASONS FOR CAUTION We measured DNAm in cord blood and not at later ages or in other tissues. Given the number of tests performed, our study power is limited and the findings need to be replicated in an independent study. WIDER IMPLICATIONS OF THE FINDINGS We find that ART is associated with DNAm differences in cord blood when compared to non-ART samples, but these differences are limited in number and effect size and have unknown functional consequences in adult blood. We did not find indications of differences between IVF and ICSI. STUDY FUNDING/COMPETING INTEREST(S) E.W.T. was supported by a VENI grant from the Netherlands Organization for Scientific Research (91617128) and JPI-H2020 Joint Programming Initiative a Healthy Diet for a Healthy Life (JPI HDHL) under proposal number 655 (PREcisE Project) through ZonMw (529051023). Financial support was provided from the European Union’s Seventh Framework Program IDEAL (259679), the Swedish Research Council (K2011-69X-21871-01-6, 2011-3060, 2015-02434 and 2018-02640) and the Strategic Research Program in Epidemiology Young Scholar Awards, Karolinska Institute (to A.N.I.) and through the Swedish Initiative for Research on Microdata in the Social And Medical Sciences (SIMSAM) framework grant no 340-2013-5867, grants provided by the Stockholm County Council (ALF-projects), the Strategic Research Program in Epidemiology at Karolinska Institutet and the Swedish Heart-Lung Foundation and Danderyd University Hospital (Stockholm, Sweden). The funders had no role in study design, data collection, analysis, decision to publish or preparation of the manuscript. The authors declare no competing interests. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Elmar W Tobi
- Periconceptional Epidemiology, Department of Obstetrics and Gynaecology, University Medical Center Rotterdam, 3015 MC GE Rotterdam, The Netherlands.,Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden.,Pediatric Allergy and Pulmonology Unit, Astrid Lindgren Children's Hospital, Stockholm 171 76, Sweden
| | - Anna Hedman
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm 182 88, Sweden
| | - Ellika Andolf
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm 182 88, Sweden
| | - Jan Holte
- Carl von Linné Clinic, Uppsala, Sweden.,Department of Women's and Children's Health, Uppsala University, Uppsala 751 85, Sweden.,Center for Reproductive Biology in Uppsala, University of Agricultural Sciences and Uppsala University, Uppsala, Sweden
| | - Jan I Olofsson
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Håkan Wramsby
- S:t Görans Sjukhus, Livio Fertilitetscentrum Kungsholmen, Stockholm 112 81, Sweden
| | - Margaretha Wramsby
- Livio Fertilitetscentrum Gärdet Storängsvägen 10, Stockholm 115 42, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Anastasia N Iliadou
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden
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29
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Castagné R, Kelly-Irving M, Krogh V, Palli D, Panico S, Sacerdote C, Tumino R, Hebels DG, Kleinjans JC, de Kok TM, Georgiadis P, Kyrtopoulos SA, Vermeulen R, Stringhini S, Vineis P, Chadeau-Hyam M, Delpierre C. A multi-omics approach to investigate the inflammatory response to life course socioeconomic position. Epigenomics 2020; 12:1287-1302. [PMID: 32875816 DOI: 10.2217/epi-2019-0261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Aim: Inflammation represents a potential pathway through which socioeconomic position (SEP) is biologically embedded. Materials & methods: We analyzed inflammatory biomarkers in response to life course SEP by integrating multi-omics DNA-methylation, gene expression and protein level in 178 European Prospective Investigation into Cancer and Nutrition-Italy participants. Results & conclusion: We identified 61 potential cis acting CpG loci whose methylation levels were associated with gene expression at a Bonferroni correction. We examined the relationships between life course SEP and these 61 cis-acting regulatory methylation sites individually and jointly using several scores. Less-advantaged SEP participants exhibit, later in life, a lower inflammatory methylome score, suggesting an overall increased expression of the corresponding inflammatory genes or proteins, supporting the hypothesis that SEP impacts adult physiology through inflammation.
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Affiliation(s)
- Raphaële Castagné
- LEASP, UMR 1027, Inserm-Université Toulouse III Paul Sabatier, Toulouse, France
| | | | - Vittorio Krogh
- Epidemiology & Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy
| | - Domenico Palli
- Cancer Risk Factors & Lifestyle Epidemiology Unit, Institute for Cancer Research Prevention & Clinical Network-ISPRO, Florence 50141, Italy
| | - Salvatore Panico
- Department of Clinical Medicine & Surgery, University of Naples Federico II, Naples 80131, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città della Salute e della Scienza University-Hospital & Center for Cancer Prevention (CPO), Turin 10133, Italy
| | - Rosario Tumino
- Cancer Registry & Department of Histopathology, Provicial Health Authority (ASP) Ragusa 97100, Italy
| | - Dennie Gaj Hebels
- MERLN Institute, Maastricht University, Universiteitssingel 40, 6229ER Maastricht, The Netherlands
| | - Jos Cs Kleinjans
- Department of Toxicogenomics, GROW Institute & Developmental Biology, Maastricht University, Maastricht 6211LK, The Netherlands
| | - Theo McM de Kok
- Department of Toxicogenomics, GROW Institute & Developmental Biology, Maastricht University, Maastricht 6211LK, The Netherlands
| | - Panagiotis Georgiadis
- National Hellenic Research Foundation, Institute of Chemical Biology, Vas. Constantinou 48, 11635 Athens, Greece
| | - Soterios A Kyrtopoulos
- National Hellenic Research Foundation, Institute of Chemical Biology, Vas. Constantinou 48, 11635 Athens, Greece
| | - Roel Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80178, 3508 TD, Utrecht, The Netherlands
| | - Silvia Stringhini
- Institute of Social & Preventive Medicine, Lausanne University Hospital, Lausanne 1010, Switzerland
| | - Paolo Vineis
- MRC-PHE Centre for Environment & Health, School of Public Health, Department of Epidemiology & Biostatistics, Imperial College London, SW7 2BU, London, UK.,Molecular & Genetic Epidemiology Unit, Italian Institute for Genomic Medicine (IIGM), Torino 10126, Italy
| | - Marc Chadeau-Hyam
- MRC-PHE Centre for Environment & Health, School of Public Health, Department of Epidemiology & Biostatistics, Imperial College London, SW7 2BU, London, UK
| | - Cyrille Delpierre
- LEASP, UMR 1027, Inserm-Université Toulouse III Paul Sabatier, Toulouse, France
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30
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Minică CC, Boomsma DI, Dolan CV, de Geus E, Neale MC. Empirical comparisons of multiple Mendelian randomization approaches in the presence of assortative mating. Int J Epidemiol 2020; 49:1185-1193. [PMID: 32155257 PMCID: PMC7660149 DOI: 10.1093/ije/dyaa013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 01/23/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Mendelian randomization (MR) is widely used to unravel causal relationships in epidemiological studies. Whereas multiple MR methods have been developed to control for bias due to horizontal pleiotropy, their performance in the presence of other sources of bias, like non-random mating, has been mostly evaluated using simulated data. Empirical comparisons of MR estimators in such scenarios have yet to be conducted. Pleiotropy and non-random mating have been shown to account equally for the genetic correlation between height and educational attainment. Previous studies probing the causal nature of this association have produced conflicting results. METHODS We estimated the causal effect of height on educational attainment in various MR models, including the MR-Egger and the MR-Direction of Causation (MR-DoC) models that correct for, or explicitly model, horizontal pleiotropy. RESULTS We reproduced the weak but positive association between height and education in the Netherlands Twin Register sample (P= 3.9 × 10-6). All MR analyses suggested that height has a robust, albeit small, causal effect on education. We showed via simulations that potential assortment for height and education had no effect on the causal parameter in the MR-DoC model. With the pleiotropic effect freely estimated, MR-DoC yielded a null finding. CONCLUSIONS Non-random mating may have a bearing on the results of MR studies based on unrelated individuals. Family data enable tests of causal relationships to be conducted more rigorously, and are recommended to triangulate results of MR studies assessing pairs of traits leading to non-random mate selection.
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Affiliation(s)
- Camelia C Minică
- Department of Biological Psychology, Vrije Universiteit, Amsterdam The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Amsterdam The Netherlands
| | - Conor V Dolan
- Department of Biological Psychology, Vrije Universiteit, Amsterdam The Netherlands
| | - Eco de Geus
- Department of Biological Psychology, Vrije Universiteit, Amsterdam The Netherlands
| | - Michael C Neale
- Department of Biological Psychology, Vrije Universiteit, Amsterdam The Netherlands
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
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31
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Jeremias G, Gonçalves FJM, Pereira JL, Asselman J. Prospects for incorporation of epigenetic biomarkers in human health and environmental risk assessment of chemicals. Biol Rev Camb Philos Soc 2020; 95:822-846. [PMID: 32045110 DOI: 10.1111/brv.12589] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 12/18/2022]
Abstract
Epigenetic mechanisms have gained relevance in human health and environmental studies, due to their pivotal role in disease, gene × environment interactions and adaptation to environmental change and/or contamination. Epigenetic mechanisms are highly responsive to external stimuli and a wide range of chemicals has been shown to determine specific epigenetic patterns in several organisms. Furthermore, the mitotic/meiotic inheritance of such epigenetic marks as well as the resulting changes in gene expression and cell/organismal phenotypes has now been demonstrated. Therefore, epigenetic signatures are interesting candidates for linking environmental exposures to disease as well as informing on past exposures to stressors. Accordingly, epigenetic biomarkers could be useful tools in both prospective and retrospective risk assessment but epigenetic endpoints are currently not yet incorporated into risk assessments. Achieving a better understanding on this apparent impasse, as well as identifying routes to promote the application of epigenetic biomarkers within environmental risk assessment frameworks are the objectives of this review. We first compile evidence from human health studies supporting the use of epigenetic exposure-associated changes as reliable biomarkers of exposure. Then, specifically focusing on environmental science, we examine the potential and challenges of developing epigenetic biomarkers for environmental fields, and discuss useful organisms and appropriate sequencing techniques to foster their development in this context. Finally, we discuss the practical incorporation of epigenetic biomarkers in the environmental risk assessment of chemicals, highlighting critical data gaps and making key recommendations for future research within a regulatory context.
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Affiliation(s)
- Guilherme Jeremias
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Fernando J M Gonçalves
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Joana L Pereira
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jana Asselman
- Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit - GhEnToxLab, Ghent University, 9000, Gent, Belgium
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32
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van Dongen J, Zilhão NR, Sugden K, Hannon EJ, Mill J, Caspi A, Agnew-Blais J, Arseneault L, Corcoran DL, Moffitt TE, Poulton R, Franke B, Boomsma DI. Epigenome-wide Association Study of Attention-Deficit/Hyperactivity Disorder Symptoms in Adults. Biol Psychiatry 2019; 86:599-607. [PMID: 31003786 PMCID: PMC6717697 DOI: 10.1016/j.biopsych.2019.02.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Previous studies have reported associations between attention-deficit/hyperactivity disorder symptoms and DNA methylation in children. We report the first epigenome-wide association study meta-analysis of adult attention-deficit/hyperactivity disorder symptoms, based on peripheral blood DNA methylation (Infinium HumanMethylation450K array) in three population-based adult cohorts. METHODS An epigenome-wide association study was performed in the Netherlands Twin Register (N = 2258, mean age 37 years), Dunedin Multidisciplinary Health and Development Study (N = 800, age 38 years), and Environmental Risk Longitudinal Twin Study (N = 1631, age 18 years), and results were combined through meta-analysis (total sample size N = 4689). Region-based analyses accounting for the correlation between nearby methylation sites were also performed. RESULTS One epigenome-wide significant differentially methylated position was detected in the Dunedin study, but meta-analysis did not detect differentially methylated positions that were robustly associated across cohorts. In region-based analyses, six significant differentially methylation regions (DMRs) were identified in the Netherlands Twin Register, 19 in the Dunedin study, and none in the Environmental Risk Longitudinal Twin Study. Of these DMRs, 92% were associated with methylation quantitative trait loci, and 68% showed moderate to large blood-brain correlations for DNA methylation levels. DMRs included six nonoverlapping DMRs (three in the Netherlands Twin Register, three in the Dunedin study) in the major histocompatibility complex, which were associated with expression of genes in the major histocompatibility complex, including C4A and C4B, previously implicated in schizophrenia. CONCLUSIONS Our findings point at new candidate loci involved in immune and neuronal functions that await further replication. Our work also illustrates the need for further research to examine to what extent epigenetic associations with psychiatric traits depend on characteristics such as age, comorbidities, exposures, and genetic background.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam.
| | - Nuno R Zilhão
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke University, Durham, North Carolina; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
| | - Eilis J Hannon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Avshalom Caspi
- Department of Psychology and Neuroscience, Duke University, Durham, North Carolina; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina; Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Jessica Agnew-Blais
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience, Duke University, Durham, North Carolina; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina; Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam
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33
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de Zeeuw EL, Kan KJ, van Beijsterveldt CEM, Mbarek H, Hottenga JJ, Davies GE, Neale MC, Dolan CV, Boomsma DI. The moderating role of SES on genetic differences in educational achievement in the Netherlands. NPJ SCIENCE OF LEARNING 2019; 4:13. [PMID: 31508241 PMCID: PMC6722095 DOI: 10.1038/s41539-019-0052-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 06/19/2019] [Indexed: 05/05/2023]
Abstract
Parental socioeconomic status (SES) is a strong predictor of children's educational achievement (EA), with an increasing effect throughout development. Inequality in educational outcomes between children from different SES backgrounds exists in all Western countries. It has been proposed that a cause of this inequality lies in the interplay between genetic effects and SES on EA, which might depend on society and the equality of the education system. This study adopted two approaches, a classical twin design and polygenic score (PGS) approach, to address the effect of parental SES on EA in a large sample of 12-year-old Dutch twin pairs (2479 MZ and 4450 DZ twin pairs with PGSs for educational attainment available in 2335 children) from the Netherlands Twin Register (NTR). The findings of this study indicated that average EA increased with increasing parental SES. The difference in EA between boys and girls became smaller in the higher SES groups. The classical twin design analyses based on genetic covariance structure modeling pointed to lower genetic, environmental, and thus phenotypic variation in EA at higher SES. Independent from a child's PGS, parental SES predicted EA. However, the strength of the association between PGS and EA did not depend on parental SES. In a within-family design, the twin with a higher PGS scored higher on EA than the co-twin, demonstrating that the effect of the PGS on EA was at least partly independent from parental SES. To conclude, EA depended on SES both directly and indirectly, and SES moderated the additive genetic and environmental components of EA. Adding information from PGS, in addition to parental SES, improved the prediction of children's EA.
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Affiliation(s)
- Eveline L. de Zeeuw
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, VUmc, Amsterdam, the Netherlands
| | - Kees-Jan Kan
- College of Child Development and Education, University of Amsterdam, Amsterdam, the Netherlands
| | - Catharina E. M. van Beijsterveldt
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, VUmc, Amsterdam, the Netherlands
| | - Hamdi Mbarek
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Qatar Genome Programme, Qatar Foundation, Doha, Qatar
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, VUmc, Amsterdam, the Netherlands
| | - Gareth E. Davies
- Avera Institute for Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD USA
| | - Michael C. Neale
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA USA
| | - Conor V. Dolan
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, VUmc, Amsterdam, the Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, VUmc, Amsterdam, the Netherlands
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Sayols-Baixeras S, Fernández-Sanlés A, Prats-Uribe A, Subirana I, Plusquin M, Künzli N, Marrugat J, Basagaña X, Elosua R. Association between long-term air pollution exposure and DNA methylation: The REGICOR study. ENVIRONMENTAL RESEARCH 2019; 176:108550. [PMID: 31260916 DOI: 10.1016/j.envres.2019.108550] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 05/17/2023]
Abstract
INTRODUCTION Limited evidence suggests that epigenetic mechanisms may partially mediate the adverse effects of air pollution on health. Our aims were to identify new genomic loci showing differential DNA methylation associated with long-term exposure to air pollution and to replicate loci previously identified in other studies. METHODS A two-stage epigenome-wide association study was designed: 630 individuals from the REGICOR study were included in the discovery and 454 participants of the EPIC-Italy study in the validation stage. DNA methylation was assessed using the Infinium HumanMethylation450 BeadChip. NOX, NO2, PM10, PM2.5, PMcoarse, traffic intensity and traffic load exposure were measured according to the ESCAPE protocol. A systematic review was undertaken to identify those cytosine-phosphate-guanine (CpGs) associated with air pollution in previous studies and we screened for them in the discovery study. RESULTS In the discovery stage of the epigenome-wide association study, 81 unique CpGs were associated with air pollution (p-value <10-5) but none of them were validated in the replication sample. Furthermore, we identified 15 CpGs in the systematic review showing differential methylation with a p-value fulfilling the Bonferroni criteria and 1673 CpGs fulfilling the false discovery rate criteria, all of which were related to PM2.5 or NO2. None of them was replicated in the discovery study, in which the top hits were located in an intergenic region on chromosome 1 (cg10893043, p-value = 6.79·10-5) and in the LRRC45 and PXK genes (cg05088605, p-value = 2.15·10-04; cg16560256, p-value = 2.23·10-04). CONCLUSIONS Neither new genomic loci associated with long-term air pollution were identified, nor previously identified loci were replicated. Continued efforts to test this potential association are warranted.
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Affiliation(s)
- Sergi Sayols-Baixeras
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Alba Fernández-Sanlés
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Albert Prats-Uribe
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Preventive Medicine and Public Health Training Unit, Parc de Salut Mar-Universitat Pompeu Fabra-Agència de Salut Pública de Barcelona (UDMPiSP PSMar-UPF-ASPB), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Isaac Subirana
- CIBER Epidemiology and Public Health (CIBERESP), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Michelle Plusquin
- Department of Epidemiology and Biostatics, The School of Public Health, Imperial College London, Medical School Building, St Mary's Hospital, Norfolk Place, London, W2 1PG, United Kingdom; Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, St Mary's Campus, Imperial College, Paddington, London, W2 1PG, United Kingdom; Centre for Environmental Sciences, Hasselt University, Campus Hasselt, Martelarenlaan 42, BE3500, Hasselt, Belgium
| | - Nino Künzli
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland; University of Basel, Klingelbergstrasse 61, 4056, Basel, Switzerland
| | - Jaume Marrugat
- REGICOR Research Group, IMIM (Hospital del Mar Medical Research Institute), DR Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Xavier Basagaña
- ISGlobal (Institute for Global Health), Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Epidemiology and Public Health (CIBERESP), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Carretera de Roda 70, 08500 Vic, Catalonia, Spain.
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35
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Establishing a Twin Register: An Invaluable Resource for (Behavior) Genetic, Epidemiological, Biomarker, and ‘Omics’ Studies. Twin Res Hum Genet 2018; 21:239-252. [DOI: 10.1017/thg.2018.23] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Twin registers are wonderful research resources for research applications in medical and behavioral genetics, epidemiology, psychology, molecular genetics, and other areas of research. New registers continue to be launched all over the world as researchers from different disciplines recognize the potential to boost and widen their research agenda. In this article, we discuss multiple aspects that need to be taken into account when initiating a register, from its preliminary sketch to its actual development. This encompasses aspects related to the strategic planning and key elements of research designs, promotion and management of a twin register, including recruitment and retaining of twins and family members of twins, phenotyping, database organization, and collaborations between registers. We also present information on questions unique to twin registers and twin-biobanks, such as the assessment of zygosity by SNP arrays, the design of (biomarker) studies involving related participants, and the analyses of clustered data. Altogether, we provide a number of basic guidelines and recommendations for reflection when planning a twin register.
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Sah P, Fanselow M, Quirk GJ, Hattie J, Mattingley J, Tokuhama-Espinosa T. The nature and nurture of education. NPJ SCIENCE OF LEARNING 2018; 3:6. [PMID: 30631467 PMCID: PMC6220266 DOI: 10.1038/s41539-018-0023-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/15/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Pankaj Sah
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Michael Fanselow
- Staglin Center for Brain and Behavioral Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Gregory J. Quirk
- School of Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - John Hattie
- Graduate School of Education, The University of Melbourne, Parkville, Australia
| | - Jason Mattingley
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Tracey Tokuhama-Espinosa
- Applied Educational Research Center, Latin American School of Social Sciences, Harvard Extension School, Harvard University, Cambridge, MA USA
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